The Facts On File

DICTIONARYof

ORGANIC CHEMISTRY

The Facts On File

DICTIONARYof

ORGANIC CHEMISTRY

Edited byJohn Daintith

The Facts On File Dictionary of Organic Chemistry

Copyright 2004 by Market House Books Ltd

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Library of Congress Cataloging-in-Publication Data

The Facts on File dictionary of organic chemistry / edited by John Daintith.p. cm.

Includes bibliographical references.ISBN 0-8160-4928-9 (alk. paper).1. ChemistryDictionaries. I. Title: Dictionary of organic chemistry. II. Daintith,

John.

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This book is printed on acid-free paper

CONTENTS

Preface vii

Entries A to Z 1

Appendixes

I. Carboxylic Acids 233

II. Amino Acids 235

III. Sugars 238

IV. Nitrogenous Bases and

Nucleosides 239

V. The Chemical Elements 241

VI. The Periodic Table 243

VII. The Greek Alphabet 244

VIII. Fundamental Constants 245

IX. Webpages 246

Bibliography 247

vii

PREFACE

This dictionary is one of a series covering the terminology and concepts usedin important branches of science. The Facts on File Dictionary of OrganicChemistry has been designed as an additional source of information for stu-dents taking Advanced Placement (AP) Science courses in high schools. Itwill also be helpful to older students taking introductory college courses.

This volume covers organic chemistry and includes basic concepts, classes ofcompound, reaction mechanisms, and important named organic com-pounds. In addition, we have included a number of compounds that are im-portant in biochemistry, as well as information on certain key biochemicalpathways. The definitions are intended to be clear and informative and,where possible, we have illustrations of chemical structures. The book alsohas a selection of short biographical entries for people who have made im-portant contributions to the field. There are a number of appendixes, in-cluding structural information on carboxylic acids, amino acids, sugars, andnitrogenous bases and nucleosides. There is also a list of all the chemical el-ements and a periodic table. The appendixes also include a short list of use-ful webpages and a bibliography.

The book will be a helpful additional source of information for anyonestudying the AP Chemistry course, especially the section on DescriptiveChemistry. It will also be useful to students of AP Biology.

ACKNOWLEDGMENTS

Contributors

John O. E. Clark B.Sc.Richard Rennie B.Sc., Ph.D.

ABA See abscisic acid.

abscisic acid (ABA) A PLANT HORMONEonce thought to be responsible for theshedding (abscission) of flowers and fruitand for the onset of dormancy in buds(hence its early name, dormin). The com-pound is associated with the closing ofpores (stoma) in the leaves of plants de-prived of water.

absolute alcohol Pure alcohol (ethanol).

absolute configuration A particularmolecular configuration of a CHIRAL mol-ecule, as denoted by comparison with a ref-erence molecule or by some sequence rule.There are two systems for expressing ab-solute configuration in common use: theDL convention and the RS convention.See optical activity.

absolute temperature Symbol: T Atemperature defined by the relationship:

T = + 273.15where is the Celsius temperature. The ab-solute scale of temperature was a funda-mental scale based on Charles law, whichapplies to an ideal gas:

V = V0(1 + )where V is the volume at temperature , V0the volume at 0, and the thermal expan-sivity of the gas. At low pressures (wherereal gases show ideal behavior) has thevalue 1/273.15. Therefore, at = 273.15the volume of the gas theoretically be-comes zero. In practice substances becomesolids at these temperatures; however, theextrapolation can be used for a scale oftemperature on which 273.15C cor-responds to 0 (absolute zero). The scale isalso known as the ideal-gas scale; on it

temperature intervals were called degreesabsolute (A) or degrees Kelvin (K), andwere equal to the Celsius degree. It can beshown that the absolute temperature scaleis identical to the currently used thermody-namic temperature scale (on which the unitis the KELVIN).

absolute zero The zero value of ther-modynamic temperature; 0 kelvin or273.15C. See absolute temperature.

absorption 1. A process in which a gasis taken up by a liquid or solid, or in whicha liquid is taken up by a solid. In absorp-tion, the substance absorbed goes into thebulk of the material. Solids that absorbgases or liquids often have a porous struc-ture. The absorption of gases in solids issometimes called sorption. There is a dis-tinction between absorption (in which onesubstance is assimilated into the bulk of an-other) and ADSORPTION (which involves at-tachment to the surface). Sometimes it isnot obvious which process is occurring.For example, a porous solid, such as acti-vated CHARCOAL may be said to absorb alarge volume of gas, but the process mayactually be adsorption on the high surfacearea of internal pores in the material.2. The process in which electromagneticradiation, particles, or sound waves loseenergy in passing through a medium. Ab-sorption involves conversion of one formof energy into another.

absorption spectrum See spectrum.

accelerator A substance that increasesthe rate of a chemical reaction. In this sensethe term is synonymous with CATALYST. Itis common to refer to catalysts as acceler-

1

A

acceptor

2

ators in certain industrial applications.For example, accelerators are used in theVULCANIZATION of rubber and in the poly-merization of adhesives. Also, in the pro-duction of composite materials usingpolyester resins a distinction is sometimesmade between the catalyst (which initiatesthe polymerization reaction) and the accel-erator (which is an additional substancemaking the catalyst more effective). Theterms promoter and activator are used in asimilar way.

acceptor The atom or group to which apair of electrons is donated in forming aCOORDINATE BOND.

accessory pigment See photosyntheticpigments.

acenaphthene (C12H10) A colorless crys-talline derivative of naphthalene, used inproducing some dyes.

acetal A type of compound formed byreaction of an alcohol with either an al-dehyde or a ketone. The first step in for-mation of an acetal is the formation of an intermediate, known as a hemiacetal.For example, ethanal (acetaldehyde;CH3CHO) reacts with ethanol (C2H5OH)as follows:

CH3CHO + C2H5OH CH(OH)(CH3)(C2H5O)

The hemiacetal has a central carbon atom(from the aldehyde) attached to a hydro-gen, a hydroxyl group, a hydrocarbongroup (CH3), and an alkoxy group(C2H5O). If a ketone is used rather than analdehyde, the resulting hemiacetal containstwo hydrocarbon groups. For example, re-action of the ketone R1COR2 with the al-cohol R3OH is:

R1COR2 + R3OH CR1R2(OH)(OR3)The formation of a hemiacetal is an exam-ple of NUCLEOPHILIC ADDITION to the car-bonyl group of the aldehyde or ketone. Thefirst step is attack of the lone pair on the Oof the alcohol on the (positively charged) Cof the carbonyl group. This is catalyzed byboth acids and bases. Acid catalysis occursby protonation of the O on the carbonyl,making the C more negative and more sus-ceptible to nucleophilic attack. In basecatalysis the OH ions from the base affectthe OH group of the alcohol, making it amore effective nucleophile.

In general, hemiacetals exist only in so-lution and cannot be isolated because theyeasily decompose back to the componentalcohol and aldehyde or ketone. However,some cyclic hemiacetals are more stable.For example, cyclic forms of SUGAR mol-ecules are hemiacetals.

Further reaction of hemiactals with an-other molecule of alcohol leads to a fullacetal. For example:

CH(OH)(CH3)(OC2H5) + C2H5OH CH(CH3)(OC2H5)2

The overall reaction of an aldehyde or ke-tone with an alcohol to give an acetal canbe written:

R1COR2 + R3OH CR1R2(OR3)2It is also possible to have mixed acetalswith the general formula CR1R2(OR3)-(OR4). Note that if the acetal is derivedfrom an aldehyde, then R1 and/or R2 maybe a hydrogen atom. The mechanism offormation of an acetal from a hemiacetal isacid catalyzed. It involves protonation ofthe OH group of the hemiacetal followedby loss of water to form an oxonium ion,which is attacked by the alcohol molecule.

Formerly it was conventional to use theterms hemiacetal and acetal for com-pounds formed by reaction between alde-hydes and alcohols. Similar reactionsbetween ketones and alcohols gave rise tocompounds called hemiketals and ketals.Current nomenclature uses hemiacetaland acetal for compounds derived fromeither an aldehyde or a ketone, but reserveshemiketal and ketal for those derivedfrom ketones. In other words, the ketalsare a subclass of the acetals and the

1 2

Acenaphthene

hemiketals are a subclass of the hemiac-etals.

acetaldehyde See ethanal.

acetamide See ethanamide.

acetate See ethanoate.

acetic acid See ethanoic acid.

acetone See propanone.

acetonitrile See methyl cyanide.

acetophenone See phenyl methyl ke-tone.

acetylation See acylation.

acetyl chloride See ethanoyl chloride.

acetylcholine (ACh) A neurotransmit-ter found at the majority of synapses,which occur where one nerve cell meets an-other.

acetylene See ethyne.

acetyl group See ethanoyl group.

acetylide See carbide.

acetyl CoA (acetyl coenzyme A) An im-portant intermediate in cell metabolism,

particularly in the oxidation of sugars,fatty acids, and amino acids, and in certainbiosynthetic pathways. It is formed by thereaction between pyruvate (from GLYCOLY-SIS) and COENZYME A, catalyzed by the en-zyme pyruvate dehydrogenase. The acetylgroup of acetyl CoA is subsequently oxi-dized in the KREBS CYCLE, to yield reducedcoenzymes and carbon dioxide. AcetylCoA is also produced in the initial oxida-tion of fatty acids and some amino acids.Other key roles for acetyl CoA include theprovision of acetyl groups in biosynthesisof fatty acids, terpenoids, and other sub-stances.

acetyl coenzyme A See acetyl CoA.

acetylsalicylic acid See aspirin.

ACh See acetylcholine.

achiral Describing a molecule that doesnot have chiral properties; i.e. one thatdoes not exhibit OPTICAL ACTIVITY.

acid A substance than contains hydro-gen and dissociates in solution to give hy-drogen ions:

HA H+ + AMore accurately, the hydrogen ion is sol-vated (a hydroxonium ion):

HA + H2O H3O+ + AStrong acids are completely dissociated inwater. Examples are sulfuric acid and tri-

3

acid

- -

--

NH

S

O

CH3

OHO

P OO

O

HO

O

ONH

CH3H3C

OO

OO

O P O P O CH2 O

NH2

N

NN

N

Acetyl CoA

choloroethanoic acid. Weak acids are onlypartially dissociated. Most organic car-boxylic acids are weak acids. In distinctionto an acid, a base is a compound that pro-duces hydroxide ions in water. Bases are either ionic hydroxides (e.g. NaOH) orcompounds that form hydroxide ions inwater. These may be metal oxides, for ex-ample:

Na2O + H2O 2Na+ + 2OHAmmonia, amines, and other nitrogenouscompounds can also form OH ions inwater:

NH3 + H2O NH4+ + OHAs with acids, strong bases are completelydissociated; weak bases are partially disso-ciated.

This idea of acids and bases is known asthe Arrhenius theory (named for theSwedish physical chemist Svante AugustArrhenius (18591927)).

In 1923 the Arrhenius idea of acids andbases was extended by the British chemistThomas Martin Lowry (18741936) and,independently, by the Danish physicalchemist Johannes Nicolaus Brnsted(18791947). In the LowryBrnstedtheory an acid is a compound that can do-nate a proton and a base is a compoundthat can accept a proton. Proton donatorsare called Brnsted acids (or protic acids)and proton acceptors are called Brnstedbases. For example, in the reaction:

CH3COOH + H2O CH3COO +H3O+

the CH3COOH is the acid, donating a pro-ton H+ to the water molecule. The water isthe base because it accepts the proton. Inthe reverse reaction, the H3O+ ion is theacid, donating a proton to the baseCH3COO. If two species are related byloss or gain or a proton they are describedas conjugate. So, in this example,CH3COO is the conjugate base of the acidCH3COOH and CH3COOH is the conju-gate acid of the base CH3COO.

In a reaction of an amine in water, forexample:

R3N + H2O R3NH+ + OHThe amine R3N accepts a proton fromwater and is therefore acting as a base.R3NH+ is its conjugate acid. Water donatesthe proton to the R3N and, in this case,

water is acting as an acid (H3O+ is its con-jugate base). Note that water can act asboth an acid and a base depending on thecircumstances. It can accept a proton (fromCH3COOH) and donate a proton (toR3N). Compounds of this type are de-scribed as amphiprotic.

One important aspect of theLowryBrnsted theory is that, because itinvolves proton transfers, it does not nec-essarily have to involve water. It is possibleto describe reactions in nonaqueous sol-vents, such as liquid ammonia, in terms ofacidbase reactions.

A further generalization of the idea ofacids and bases was the Lewis theory putforward, also in 1923, by the US physicalchemist Gilbert Newton Lewis (18751946). In this, an acid (a Lewis acid) is acompound that can accept a pair of elec-trons and a base (a Lewis base) is one thatdonates a pair of electrons. In a traditionalacidbase reaction, such as:

HCl + NaOH NaCl + H2Othe effective reaction is

H+ + OH H2OThe OH (base) donates an electron pair tothe H+ (acid). However, in the Lewistheory acids and bases need not involveprotons at all. For example, ammonia(NH3) adds to boron trichloride (BCl3) toform an adduct:

NH3 + BCl3 H3NBCl3Here, ammonia is the Lewis base donatinga LONE PAIR of electrons to boron trichlor-ide (the Lewis acid).

The concept of acidbase reactions is animportant generalization in chemistry, andthe Lewis theory connects it to two othergeneral ideas. One is oxidationreduction:oxidation involves loss of electrons and re-duction involves gain of electrons. Also, inorganic chemistry, it is connected with theidea of electrophilenucleophile reactions.Acids are ELECTROPHILES and bases are NU-CLEOPHILES. In organic chemistry a numberof inorganic halides, such as AlCl3 andTiCl4, are important Lewis acids, formingintermediates in such processes as theFRIEDELCRAFTS REACTION.

acid anhydride A type of organic com-pound containing the group CO.O.CO.

acid anhydride

4

Simple acid anhydrides have the generalformula RCOOCOR, where R and R arealkyl or aryl groups. They can be regardedas formed by removing a molecule of waterfrom two molecules of carboxylic acid. Forexample, ethanoic anhydride comes fromethanoic acid:

2CH3COOH H2O CH3CO.O.COCH3

A long-chain dicarboxylic acid may alsoform a cyclic acid anhydride, in which theCO.O.CO group forms part of a ring.Acid anhydrides can be prepared by reac-tion of an acyl halide with the sodium saltof a carboxylic acid, e.g.:

RCOCl + RCOONa+ RCOOCOR + NaCl

Like the acyl halides, they are very reactiveacylating agents. They hydrolyze readily tocarboxylic acids:

RCOOCOR + H2O RCOOH + RCOOH

See also acylation; anhydride.

acid dyes The sodium salts of organicacids used in the dyeing of silk and wool.They are so called because they are appliedfrom a bath acidified with dilute sulfuric orethanoic acid.

acid halide See acyl halide.

acidic Having a tendency to release aproton or to accept an electron pair from adonor. In aqueous solutions the pH is ameasure of the acidity, i.e. an acidic solu-tion is one in which the concentration ofH3O+ exceeds that in pure water at thesame temperature; i.e. the pH is lower than7. A pH of 7 indicates a neutral solution.

acidic hydrogen A hydrogen atom in amolecule that enters into a dissociationequilibrium when the molecule is dissolvedin a solvent. For example, in ethanoic acid(CH3COOH) the acidic hydrogen is theone on the carboxyl group, COOH:

CH3COOH + H2O CH3COO + H3O+.

acidity constant See dissociation con-stant.

acid value A measure of the free acidpresent in fats, oils, resins, plasticizers, andsolvents, defined as the number of mil-ligrams of potassium hydroxide requiredto neutralize the free acids in one gram ofthe substance.

acridine (C12H9N) A colorless crys-talline heterocyclic compound with threefused rings. Derivatives of acridine areused as dyes and biological stains.

Acrilan (Trademark) A synthetic fiberthat consists of a copolymer of 1-cyanoethene (acrylonitrile; vinyl cyanide)and ethenyl ethanoate (vinyl acetate). Seeacrylic resin.

acrolein See propenal.

acrylic acid See propenoic acid.

acrylic resin A synthetic resin made bypolymerizing an amide, nitrile, or ester de-rivative of 2-propenoic acid (acrylic acid).Acrylic resins (known as acrylics) areused in a variety of ways. A common ex-ample is poly(methylmethacrylate), whichis produced by polymerizing methylmethacrylate, CH2:CH(CH3)COOCH3.This is the clear material sold as Plexiglas.Another example is the compound methyl2-cyanoacrylate, CH2:CH(CN)COOCH3.This polymerizes very readily in air and isthe active constituent of superglue. Inboth these cases there is a double C=Cbond conjugated with the carbonyl C=Obond and the polymerization has a free-radical mechanism. The free election is onthe carbon atom next to the carbonylgroup, which stabilizes the radical. An-other example of an acrylic polymer isformed by free-radical polymerization of

5

acrylic resin

NNN

Acridine

acrylonitrile (CH2:CHCN) to give poly-(acrylonitrile). This is used in syntheticfibers (such as Acrilan). In this case the un-paired electron is on the carbon next to theCN group. Acrylic resins are also used inpaints.

acrylonitrile See propenonitrile.

actinic radiation Radiation that cancause a chemical reaction; for example,ultraviolet radiation is actinic.

actinomycin Any of a number of antibi-otics produced by certain bacteria. Themain one, actinomycin D (or dactino-mycin), can bind between neighbouringbase pairs in DNA, preventing RNA syn-thesis. It is used in the treatment of somecancers.

action spectrum A graph showing theeffect of different wavelengths of radia-tion, usually light, on a given process. It is often similar to the ABSORPTION SPEC-TRUM of the substance that absorbs the ra-diation and can therefore be helpful inidentifying that substance. For example,the action spectrum of photosynthesis issimilar to the absorption spectrum ofchlorophyll.

activated charcoal See charcoal.

activated complex The partially bondedsystem of atoms in the TRANSITION STATE ofa chemical reaction.

activation energy Symbol: Ea The min-imum energy a system must acquire beforea chemical reaction can occur, regardlessof whether the reaction is exothermic orendothermic. Activation energy is oftenrepresented as an energy barrier that has tobe overcome if a reaction is to take place.See also Arrhenius equation; transitionstate.

activator See accelerator.

active mass See mass action.

active site 1. A site on the surface of a

solid catalyst at which catalytic activity oc-curs or at which the catalyst is particularlyeffective.2. The region of an ENZYME molecule thatcombines with and acts on the substrate. Itconsists of catalytic amino acids arrangedin a configuration specific to a particularsubstrate or type of substrate. The onesthat are in direct combination are the con-tact amino acids. Other amino acids maybe further away but still play a role in theaction of the enzyme. These are auxilliaryamino acids. Binding of a regulatory com-pound to a separate site, known as the AL-LOSTERIC SITE, on the enzyme molecule maychange this configuration and hence the ef-ficiency of the enzyme activity.

activity 1. Symbol: a Certain thermody-namic properties of a solvated substanceare dependent on its concentration (e.g. itstendency to react with other substances).Real substances show departures fromideal behavior and a corrective concentra-tion term the activity has to be intro-duced into equations describing realsolvated systems.2. Symbol: A The average number of atomsdisintegrating per unit time in a radioactivesubstance.

activity coefficient Symbol: f A meas-ure of the degree of deviation from idealityof a dissolved substance, defined as:

a = fc

acrylonitrile

6

ener

gy

A ... B ... C

AB C

AB C

H

reaction coordinate

Activation energy

where a is the activity and c the concentra-tion. For an ideal solute f = 1; for real sys-tems f can be less or greater than unity.

acyclic Describing a compound that isnot cyclic (i.e. a compound that does notcontain a ring in its molecules).

acyl anhydride See acid anhydride.

acylating agent See acylation.

acylation Any reaction that introducesan acyl group (RCO) into a compound.Acylating agents are compounds such asacyl halides (RCOX) and acid anhydrides(RCOOCOR), which react with such nu-cleophiles as H2O, ROH, NH3, andRNH2. In these reactions a hydrogen atomof a hydroxyl or amine group is replacedby the RCO group. In acetylation theacetyl group (CH3CO) is used. In benzoy-lation the benzoyl group (C6H5CO) isused. Acylation is used to prepare crys-talline derivatives of organic compounds toidentify them (e.g. by melting point) andalso to protect OH groups in synthetic re-actions.

acyl group The group of atoms RCO.

acyl halide (acid halide) A type of or-ganic compound of the general formulaRCOX, where X is a halogen (acyl chlo-ride, acyl bromide, etc.).

Acyl halides can be prepared by the re-action of a carboxylic acid with a halo-genating agent. Commonly, phosphorushalides are used (e.g. PCl5) or a sulfur di-halide oxide (e.g. SOCl2):

RCOOH + PCl5 RCOCl + POCl3 + HCl

RCOOH + SOCl2 RCOCl + SO2 + HCl

The acyl halides have irritating vaporsand fume in moist air. They are very reac-tive to the hydrogen atom of compoundscontaining hydroxyl (OH) or amine(NH2) groups. For example, the acylhalide ethanoyl chloride (acetyl chloride;CH3COCl) reacts with water to give a car-boxylic acid (ethanoic acid):

CH3COCl + H2O CH3COOH + HClWith an alcohol (e.g. ethanol) it gives anester (ethyl ethanoate):

CH3COCl + C2H5OH CH3COOC2H5 + HCl

With ammonia it gives an amide(ethanamide; acetamide):

CH3COCl + NH3 CH3CONH2 + HCl

With an amine (e.g. methylamine) it givesan N-substituted amine (N-methyl ethana-mide)

CH3COCl + CH3NH2 CH3CONH(CH3)

See also acylation.

addition polymerization See polymer-ization.

addition reaction A reaction in whichadditional atoms or groups of atoms are in-troduced into an unsaturated compound,such as an alkene, alkyne, aldehyde, or ke-tone. A simple example is the addition ofbromine across the double bond in ethene:

H2C:CH2 + Br2 BrH2CCH2BrAddition reactions can occur by additionof electrophiles or nucleophiles. See elec-trophilic addition; nucleophilic addition.

adduct See coordinate bond.

adenine A nitrogenous base found inDNA and RNA. It is also a constituent ofcertain coenzymes, and when combinedwith the sugar ribose it forms the nucleo-side adenosine found in AMP, ADP, andATP. Adenine has a purine ring structure.See also DNA.

adenosine (adenine nucleoside) A NU-CLEOSIDE formed from adenine linked to D-ribose with a -glycosidic bond. It is widelyfound in all types of cell, either as the freenucleoside or in combination in nucleic

7

adenosine

N

N N

N

NH2

H

713

6

9

Adenine

acids. Phosphate esters of adenosine, suchas ATP, are important carriers of energy inbiochemical reactions.

adenosine diphosphate See ADP.

adenosine monophosphate See AMP.

adenosine triphosphate See ATP.

adiabatic change A change for whichno energy enters or leaves the system. In anadiabatic expansion of a gas, mechanicalwork is done by the gas as its volume in-creases and the gas temperature falls. Foran ideal gas undergoing a reversible adia-batic change it can be shown that

pV = K1Tp1 = K2

and TV1 = K3where K1, K2, and K3 are constants and isthe ratio of the principal specific heat ca-pacities. Compare isothermal change.

adipic acid See hexanedioic acid.

adjacent Designating atoms or bondsthat are next to each other in a molecule.

ADP (adenosine diphosphate) A nu-cleotide consisting of adenine and ribosewith two phosphate groups attached. Seealso ATP.

adrenalin See epinephrine.

adsorbate A substance that is adsorbedon a surface. See adsorption.

adsorbent Having a tendency to adsorb.As a noun the adsorbent is the substance

on which adsorption takes place. See ad-sorption.

adsorption A process in which a layerof atoms or molecules of one substanceforms on the surface of a solid or liquid. Allsolid surfaces take up layers of gas from thesurrounding atmosphere. The adsorbedlayer may be held by chemical bonds(chemisorption) or by weaker van derWaals forces (physisorption).Compare absorption.

aerobic Describing a biochemical processthat takes place only in the presence of freeoxygen. Compare anaerobic.

aerobic respiration (oxidative metabo-lism) Respiration in which free oxygen isused to oxidize organic substrates to car-bon dioxide and water, with a high yield ofenergy. Carbohydrates, fatty acids, and ex-cess amino acids are broken down yieldingacetyl CoA and the reduced coenzymesNADH and FADH2. The acetyl coenzymeA enters a cyclic series of reactions, theKREBS CYCLE, with the production of car-bon dioxide and further molecules ofNADH and FADH2. NADH and FADH2are passed to the ELECTRON-TRANSPORTCHAIN (involving cytochromes and flavo-proteins), where they combine with atomsof free oxygen to form water. Energy re-leased at each stage of the chain is used toform ATP during a coupling process. Thesubstrate is completely oxidized and thereis a high energy yield. There is a net pro-duction of 38 ATPs per molecule of glucoseduring aerobic respiration, a yield of about19 times that of anaerobic respiration.Aerobic respiration is therefore the pre-ferred mechanism of the majority of organ-isms. See also oxidative phosphorylation;respiration.

aerosol See sol.

affinity The extent to which one sub-stance reacts with another in a chemicalchange.

afterdamp See firedamp.

adenosine diphosphate

8

N

N N

N

NH2

OHOCH2

OH OHAdenosine

agent orange A herbicide consisting ofa mixture of two weedkillers (2,4-D and2,4,5-T). It was designed for use in chemi-cal warfare to defoliate trees in areas wherean enemy may be hiding or to destroyenemy crops. Agent orange, so-called fromthe orange-colored canisters in which itwas supplied, was first used by US forcesduring the Vietnam war. It contains tracesof the highly toxic chemical DIOXIN, whichcauses cancers and birth defects.

air gas See producer gas.

alanine See amino acid.

albumen The white of an egg, whichconsists mainly of the protein ALBUMIN.

albumin A soluble protein that occurs inmany animal fluids, such as blood serumand egg white.

alcohol A type of organic compound ofthe general formula ROH, where R is a hy-drocarbon group. Examples of simple alco-hols are methanol (CH3OH) and ethanol(C2H5OH). Alcohols have the OH groupattached to a carbon atom that is part of analkyl group. If the carbon atom is part of

9

alcohol

primary (ethanol)

secondary (propan-2-ol)

tertiary (2-methylpropan-2-ol)

C

H OH

HCH3

C

H3C OH

HH3C

C

H3C OH

CH3H3C

Alcohol

glucose

glycolysis2 ATP

38 ATP

34 ATP

respiratory chainH2O

O2

H

2 ATP

Krebscycle

CO2

acetyl CoA

pyruvate

Aerobic respiration

an aromatic ring, as in PHENOL, C6H5OH,the compound does not have the character-istic properties of alcohols. Phenyl-methanol (C6H5CH2OH) does have thecharacteristic properties of alcohols (in thiscase the carbon atom to which the OH isattached is not part of the aromatic ring).

Alcohols can have more than one OHgroup; those containing two, three, ormore such groups are described as dihy-dric, trihydric, and polyhydric respectively(as opposed to alcohols containing oneOH group, which are monohydric). Forexample, ethane-1,2-diol (ethylene glycol;(HOCH2CH2OH) is a dihydric alcoholand propane-1,2,3-triol (glycerol;HOCH2CH(OH)CH2OH) is a trihydric al-cohol. Dihydric alcohols are known asdiols; trihydric alcohols as triols, etc. Ingeneral, alcohols are named by using thesuffix -ol with the name of the parent hy-drocarbon.

Alcohols are further classified accord-ing to the environment of the COHgrouping. If the carbon atom is attached totwo hydrogen atoms, the compound is aprimary alcohol. If the carbon atom is at-tached to one hydrogen atom and twoother groups, it is a secondary alcohol. Ifthe carbon atom is attached to three othergroups, it is a tertiary alcohol. Alcohols canbe prepared by:1. Hydrolysis of haloalkanes using aque-

ous potassium hydroxide:RI + OH ROH + I

2. Reduction of aldehydes by nascent hy-drogen (e.g. from sodium amalgam inwater):

RCHO +2[H] RCH2OHThe main reactions of alcohols are:1. Oxidation by potassium dichromate(VI)

in sulfuric acid. Primary alcohols givealdehydes, which are further oxidized tocarboxylic acids:

RCH2OH RCHO RCOOH1. Secondary alcohols are oxidized to ke-

tones.R1R2CHOH R1R2CO

2. Formation of esters with acids. The re-action, which is reversible, is catalyzedby H+ ions:

ROH + RCOOH RCOOR + H2O

3. Dehydration over hot pumice (400C)to alkenes:

RCH2CH2OH H2O RCH:CH24. Reaction with sulfuric acid. Two types

of reaction are possible. With excessacid at 160C dehdyration occurs togive an alkene:

RCH2CH2OH + H2SO4 H2O + RCH2CH2.HSO4

RCH2CH2.HSO4 RCH:CH2 + H2SO4

4. With excess alcohol at 140C an ether isformed:

2ROH ROR + H2OSee also acetal; acylation; Grignardreagent.

aldaric acid See sugar acid.

aldehyde A type of organic compoundwith the general formula RCHO, wherethe CHO group (the aldehyde group) con-sists of a carbonyl group attached to a hy-drogen atom. Simple examples ofaldehydes are methanal (formaldehyde;HCHO) and ethanal (acetaldehyde; CH3-CHO).

Aldehydes are formed by oxidizing aprimary alcohol; in the laboratory potas-sium dichromate(VI) is used in sulfuricacid. They can be further oxidized to car-boxylic acids. Reduction (using a catalystor nascent hydrogen from sodium amal-gam in water) produces the parent alcohol.For example, oxidation of ethanol(C2H5OH) gives ethanal (acetaldehyde;CH3CHO):

C2H5OH + [O] CH3CHO + H2OFurther oxidation gives ethanoic acid(acetic acid; CH3COOH):

CH3CHO + [O] CH3COOHThe systematic method of naming alde-hydes is to use the suffix -al with the

aldaric acid

10

aldehyde group

CR

O

H

Aldehyde

name of the parent hydrocarbon. For ex-ample: methane (CH4) is the parent hydro-carbon of the alcohol methanol (CH3OH),the aldehyde methanal (HCHO), and the carboxylic acid methanoic acid(HCOOH); ethane (C2H6) is the parent hydrocarbon of the alcohol ethanol (C2H5-OH), the aldehyde ethanal (CH3CHO),and the carboxylic acid ethanoic acid(CH3COOH); etc. An older method ofnaming aldehydes is based on the name ofthe related acid. For example, methanoicacid (HCOOH) has the traditional nameformic acid and the related aldehyde(HCHO) is traditionally called formalde-hyde. Similarly, ethanoic acid (CH3OOH)is commonly known as acetic acid and thealdehyde CH3CHO is known as acetalde-hyde.Reactions of aldehydes are:1. Aldehydes are reducing agents, being

oxidized to carboxylic acids in theprocess. These reactions are used as testsfor aldehydes using such reagents asFEHLINGS SOLUTION and TOLLENSREAGENT (silver-mirror test).

2. They form addition compounds withhydrogen cyanide to give cyanohydrins.For example, propanal gives 2-hydroxy-butanonitrile:

C2H5CHO + HCN C2H5CH(OH)CN

3. They form bisulfite addition compoundswith the hydrogensulfite(IV) ion (bisul-fite; HSO3):RCHO + HSO3 RCH(OH)(HSO3)

4. They undergo condensation reactionswith such compounds as hydrazine, hy-droxylamine, and their derivatives.

5. With alcohols they form hemiacetalsand ACETALS.

6. Simple aldehydes polymerize readily.Polymethanal or methanal trimer can beformed from METHANAL depending onthe conditions. ETHANAL gives ethanaltrimer or ethanal tetramer.

See also Cannizzaro reaction; condensa-tion reaction; ketone.

Alder, Kurt (19021958) German or-ganic chemist who is noted for the processknown as the DIELSALDER REACTION. Par-ticular cases of the reaction had been

known since the 1900s but Alder and OttoDiels recognized that this mechanism isvery common. They first reported their re-sults in 1928. Alder and Diels shared the1950 Nobel Prize for chemistry for thiswork.

alditol See sugar alcohol.

aldohexose An aldose SUGAR with sixcarbon atoms.

aldol A compound that contains both analdehyde group (CHO) and an alcoholgroup (OH). See aldol reaction.

aldol reaction A reaction in which twomolecules of aldehyde combine to give analdol i.e. a compound containing bothaldehyde and alcohol functional groups.The reaction is base-catalyzed; the reactionof ethanal (acetaldehyde) refluxed withsodium hydroxide gives:

2CH3CHO CH3CH(OH)CH2CHOThe mechanism is similar to that of theCLAISEN CONDENSATION: the first step is re-moval of a proton to give a carbanion,which subsequently attacks the carbon ofthe carbonyl group on the other molecule:

CH3CHO + OH CH2CHO + H2OCH3CHO + CH2CHO CH3CH(OH)CH2CHO.

aldonic acid See sugar acid.

aldopentose An aldose SUGAR with fivecarbon atoms.

aldose A SUGAR containing an aldehydegroup (CHO) or a potential aldehydegroup.

algin See alginic acid.

alginic acid (algin; (C6H8O6)n) A yel-low-white organic solid that is found inbrown algae. It is a complex polysaccha-ride and produces, in even very dilute solu-tions, a viscous liquid. Alginic acid hasvarious uses, especially in the food industryas a stabilizer and texture agent.

11

alginic acid

alicyclic compound An aliphatic cycliccompound, such as cyclohexane or cyclo-propane.

aliphatic compound An organic com-pound with properties similar to those ofthe alkanes, alkenes, and alkynes and theirderivatives. Most aliphatic compoundshave an open chain structure but some,such as cyclohexane and sucrose, haverings (these are described as alicyclic). The term is used in distinction to ARO-MATIC COMPOUNDS, which are similar tobenzene.

alizarin (1,2-dihydroxyanthraquinone)An important orange-red organic com-pound used in the dyestuffs industry toproduce red lakes. It occurs naturally in theroot of the plant madder and may also besynthesized from anthraquinone.

alkali A water-soluble strong base.Strictly the term refers to the hydroxides ofthe alkali metals (group 1) only, but incommon usage it refers to any soluble base.Thus borax solution may be described asmildly alkaline.

alkaloid One of a group of natural or-ganic compounds found in plants. Theycontain oxygen and nitrogen atoms; mostare poisonous. However, they include anumber of important drugs with character-istic physiological effects, e.g. morphine,codeine, caffeine, cocaine, and nicotine.

alkane A type of hydrocarbon with gen-eral formula CnH2n+2. Alkanes are satu-rated compounds, containing no double ortriple bonds. Systematic names end in -ane:methane (CH4) and ethane (C2H6) are typ-ical examples. The alkanes are fairly unre-active (their former name, the paraffins,means small affinity). In ultraviolet radia-tion they react with halogens to give a mix-ture of substitution products. This involvesa free-radical chain reaction and is impor-tant as a first step in producing other com-pounds from alkanes. There are a numberof ways of preparing specific alkanes:1. From a sodium salt of a carboxylic acid

treated with sodium hydroxide:

RCOONa+ + NaOH RH + Na2CO32. By reduction of a haloalkane with

nascent hydrogen from the action ofethanol on a zinccopper couple:

RX + 2[H] RH + HX3. By the WURTZ REACTION i.e. sodium in

dry ether on a haloalkane:2RX + 2Na 2NaX + RR

4. By the KOLB ELECTROLYTIC METHOD:RCOO RR

5. By refluxing a haloalkane with magne-sium in dry ether to form a GRIGNARDREAGENT:

RI + Mg RMgI5. With acid this gives the alkane:

RMgI + H RHThe main source of lower molecularweight alkanes is natural gas (for methane)and crude oil.

alkene A type of aliphatic hydrocarboncontaining one or more double bonds inthe molecule. Alkenes with one doublebond have the general formula CnH2n. Thealkenes are unsaturated compounds. Theycan be obtained from crude oil by crackingalkanes. Systematic names end in -ene: ex-amples are ethene (C2H4) and propene(C3H6), both of which are used in plasticsproduction and as starting materials forthe manufacture of many other organicchemicals. The former general name for analkene was olefin.

The methods of synthesizing alkenesare:

alicyclic compound

12

hex-1-ene

CH3 CH2 CH2 CH2 CH2CH =

hex-2-ene

hex-3-ene

CH3 CH2 CH2 CH CH3= CH

CH3 CH2 CHCH = CH2 CH3

Alkene

1. The elimination of HBr from ahaloalkane using an alcoholic solutionof potassium hydroxide:RCH2CH2Br + KOH KBr + H2O +

RCH:CH22. The dehydration of an alcohol by pass-

ing the vapor over hot pumice (400C):RCH2CH2OH RCH:CH2 + H2O

The reactions of simple alkenes include:1. Hydrogenation using a catalyst (usually

nickel at about 150C):RCH:CH2 + H2 RCH2CH3

2. Addition reactions with halogen acids togive haloalkanes:

RCH:CH2 + HX RCH2CH2X2. The addition follows MARKOVNIKOFFS

RULE.3. Addition reactions with halogens, e.g.

RCH:CH2 + Br2 RCHBrCH2Br4. Hydration using concentrated sulfuric

acid, followed by dilution and warming:RCH:CH2 + H2O RCH(OH)CH3

5. Oxidation by cold potassium perman-ganate solutions to give diols:

RCH:CH2 + H2O + [O] RCH(OH)CH2OH

6. Oxidation to form cyclic epoxides (oxi-ranes). Ethene can be oxidized in airusing a silver catalyst to the cyclic com-pound epoxyethane (C2H4O). Moregenerally peroxy carboxylic acids areused as the oxidizing agent.

7. Polymerization to polyethene (by theZIEGLER PROCESS or PHILLIPS PROCESS).

See also oxo process; ozonolysis.In general, addition to simple alkenes is

ELECTROPHILIC ADDITION. Attack is by anelectrophile on the pi orbital of the alkene.In the case of attack by a halogen acid (e.g.HBr), the initial reaction is by the (positive)hydrogen giving a positively charged inter-mediate ion (carbocation) and a Br ion.The Br ion then attacks the intermediatecarbocation. In the case of a halogen (e.g.Br2) the bromine acts as an electrophile toform an initial cyclic positively chargedbromonium ion and a negative Br ion. TheBr ion further attacks the bromonium ionto give the substituted product.

alkoxide An organic compound con-taining an ion of the type RO, where R isan alkyl group. Alkoxides can be made by

the reaction of metallic sodium on an alco-hol. For example, ethanol reacts withsodium to give sodium ethoxide:

2C2H5OH + 2Na 2C2H5ONa+) + H2

Alkoxides are ionic compounds containingan alkoxide ion (RO). They are named ac-cording to the parent alcohol. Thus,methanol (CH3OH) gives methoxidesCH3O, ethanol (C2H5OH) gives ethoxidesC2H5O, etc.

alkoxyalkane (diethyl ether) See ether.

alkylbenzene A type of organic hydro-carbon containing one or more alkylgroups substituted onto a benzene ring.Methylbenzene (toluene; C6H5CH3) is thesimplest example. Alkylbenzenes can bemade by a FRIEDELCRAFTS REACTION or bythe WURTZ REACTION. Industrially, largequantities of methylbenzene are made fromcrude oil.

Substitution of alkylbenzenes can occurat the benzene ring; the alkyl group directsthe substituent into the 2- or 4-position.Substitution of hydrogen atoms on thealkyl group can also occur.

alkyl group A group obtained by re-moving a hydrogen atom from an alkaneor other aliphatic hydrocarbon. For exam-ple, the methyl group (CH3) is derivedfrom methane (CH4).

alkyl halide See haloalkane.

alkyl sulfide A THIOETHER with the gen-eral formula RSR, where R and R arealkyl groups.

alkyne A type of hydrocarbon contain-ing one or more triple carboncarbonbonds in its molecule. Alkynes with onetriple bond have the general formulaCnH2n2. The alkynes are unsaturated com-pounds. The simplest member of the seriesis ethyne (acetylene; C2H2), which can beprepared by the action of water on calciumdicarbide.

CaC2 + 2H2O Ca(OH)2 + C2H2The alkynes were formerly called theacetylenes.

13

alkyne

In general, alkynes can be made by thecracking of alkanes or by the action of ahot alcoholic solution of potassium hy-droxide on a dibromoalkane, for example:

BrCH2CH2Br + KOH KBr + CH2:CHBr + H2O

CH2:CHBr + KOH CHCH + KBr + H2O

The main reactions of the alkynes are:1. Hydrogenation with a catalyst (usually

nickel at about 150C):C2H2 + H2 C2H4C2H4 + H2 C2H6

2. Addition reactions with halogen acids:C2H2 + HI H2C:CHI

H2C:CHI + HI CH3CHI23. Addition of halogens; for example, with

bromine in tetrachloromethane:C2H2 + Br2 BrHC:CHBr

BrHC:CHBr + Br2 Br2HCCHBr24. With dilute sulfuric acid at 6080C and

mercury(II) catalyst, ethyne formsethanal (acetaldehyde):

C2H2 + H2O H2C:C(OH)HThis enol form converts to the alde-hyde:

CH3COH5. Ethyne polymerizes if passed through a

hot tube to produce some benzene:3C2H2 C6H6

6. Ethyne forms unstable dicarbides(acetylides) with ammoniacal solutionsof copper(I) and silver(I) chlorides.

Addition to simple alkynes is ELECTRO-PHILIC ADDITION, as with ALKENES.

allosteric site A part of an enzyme sep-arate from the active site to which a spe-cific effector or modulator can be attached.This attachment is reversible and alters theactivity of the enzyme. Allosteric enzymespossess an allosteric site in addition to theirACTIVE SITE. This site is as specific in its re-lationship to modulators as active sites areto substrates. See active site. Some iron-enzymatic proteins e.g. hemoglobin alsoundergo allosteric effects.

allyl group See propenyl group.

alpha amino acid See amino acid.

alpha helix A highly stable structure in

which peptide chains are coiled to form aspiral. Each turn of the spiral contains ap-proximately 3.6 amino-acid residues. TheR group of these amino-acids extends out-ward from the helix and the helix is heldtogether by hydrogen bonding betweensuccessive coils. If the alpha helix isstretched the hydrogen bonds are brokenbut reform on relaxation. The alpha helixis found in muscle protein and keratin. It isone of the two basic secondary structuresof PROTEINS.

alpha-naphthol test (Molischs test) Astandard test for carbohydrates in solution.Molischs reagent, alpha-naphthol in alco-hol, is mixed with the test solution. Con-centrated sulfuric acid is added and a violetring at the junction of the two liquids indi-cates the presence of carbohydrates.

alternating copolymer See polymer-ization.

aluminum trimethyl See trimethylalu-minum.

amalgam An alloy of mercury with oneor more other metals. Amalgams may beliquid or solid. An amalgam of sodium(Na/Hg) with water is used as a source ofnascent hydrogen.

amatol A high explosive that consists of

allosteric site

14

OOOHHH

CCC CCCNNN

NNN

HHH HHHOOO

HHH

CCC

CCCNNN

HHHOOO

CCC

HHHOOO

CCCNNN

HHHCCC

A

hydrogen bond

OOO

amino-acid side A

A

A

Alpha helix

a mixture of ammonium nitrate and TNT(trinitrotoluene).

amide 1. A type of organic compound ofgeneral formulae RCONH2 (primary),(RCO)2NH (secondary), and (RCO)3N(tertiary). Amides are crystalline solids andare basic in nature, some being soluble inwater. They can be formed by reaction ofammonia with acid anhydrides:

(RCO)2O + 2NH3 RCONH2 + RCOONH4+

They can also be made by reacting ammo-nia with an acyl chloride:

RCOCl + 2NH3 RCONH2 + NH4ClReactions of amides include:1. Reaction with hot acids to give car-

boxylic acids:RCONH2 + HCl + H2O

RCOOH + NH4Cl2. Reaction with nitrous acid to give car-

boxylic acids and nitrogen:RCONH2 + HNO2 RCOOH + N2 + H2O

3. Dehydration by phosphorus(V) oxide togive a nitrile:

RCONH2 H2O RCNSee also Hofmann degradation.2. An inorganic salt containing the NH2

ion. Ionic amides are formed by the reac-tion of ammonia with certain reactivemetals (such as sodium and potassium).Sodamide, NaNH2, is a common example.

amination The introduction of anamino group (NH2) into an organic com-pound. An example is the conversion of analdehyde or ketone into an amide by reac-tion with hydrogen and ammonia in thepresence of a catalyst:

RCHO + NH3 + H2 RCH2NH2 +H2O

amine A compound containing a nitro-gen atom bound to hydrogen atoms or hy-drocarbon groups. Amines have thegeneral formula R3N, where R can be hy-drogen or an alkyl or aryl group. They canbe prepared by reduction of amides ornitro compounds.

Amines are classified according to thenumber of organic groups bonded to thenitrogen atom: one, primary; two, sec-

ondary; three, tertiary. Since amines arebasic they can form the quaternary ion,R3NH+. All three types, plus a quaterniumsalt, can be produced by the HOFMANNDEGRADATION (which occurs in a sealedvessel at 100C):

RX + NH3 RNH3+ XRNH3+ X + NH3 RNH2 + NH4X

RNH2 + RX R2NH2+ XR2NH2+ X + NH3 R2NH + NH4X

R2NH + RX R3NH+ XR3NH+ X + NH3 R3N + NH4X

R3N + RX R4N+XReactions of amines include:1. Reaction with acids to form salts:

R3N + HX R3NH+X2. Reaction with acyl halides to give N-

substituted amides (primary and sec-ondary amines only):RNH2 + RCOCl RCONHR + HX

See also amine salt.

15

amine

primary (e thylamine)

secondary (diethylamine)

tertiary (triethylamine)

C2H5

H

H

N

C2H5

C2H5

H

N

C2H5

C2H5

C2H5

N

Amine

amine salt A salt similar to an ammo-nium salt, but with organic groups at-tached to the nitrogen atom. For example,triethylamine ((C2H5)3N) will react withhydrogen chloride to give triethylammo-nium chloride:

(C2H5)3N + HCl (C2H3)3NH+ClSalts of this type may have four groups onthe nitrogen atom. For example, withchloroethane, tetraethylammonium chlo-ride can be formed:

(C2H5)3N + C2H5Cl (C2H5)4N+ClSometimes amine salts are named using thesuffix -ium. For instance, aniline(C6H5NH2) forms anilinium chlorideC6H5NH3+Cl. Often insoluble alkaloidsare used in medicine in the form of theiramine salt (sometimes referred to as thehydrochloride).

amino acid A derivative of a carboxylicacid in which a hydrogen atom in analiphatic acid has been replaced by anamino group. Thus, from ethanoic acid,the amino acid 2-aminoethanoic acid(glycine) is formed. The amino acids of spe-cial interest are those that occur as con-stituents of naturally occurring PEPTIDESand PROTEINS. These all have the NH2 andCOOH groups attached to the same car-bon atom; i.e. they are alpha amino acids.All are white, crystalline, soluble in water

(but not in alcohol), and, with the sole ex-ception of the simplest member, all are op-tically active.

In the body the various proteins are as-sembled from the necessary amino acidsand it is important therefore that all theamino acids should be present in sufficientquantities. In adult humans, twelve of thetwenty amino acids can be synthesized bythe body itself. Since these are not requiredin the diet they are known as nonessentialamino acids. The remaining eight cannotbe synthesized by the body and have to besupplied in the diet. They are known as es-sential amino acids.

aminobenzene See aniline.

aminoethane See ethylamine.

amino group The group NH2.

amino sugar A sugar in which a hy-droxyl group (OH) has been replaced by anamino group (NH2). Glucosamine (fromglucose) occurs in many polysaccharides ofvertebrates and is a major component ofchitin. Galactosamine or chondrosamine(from galactose) is a major component ofcartilage and glycolipids. Amino sugars areimportant components of bacterial cellwalls.

amine salt

16

The amino acids most commonly found in proteins

alaninearginineasparagineaspartic acidcysteineglutamic acidglutamine

glycinehistidine*isoleucine*leucine*lysine*methionine*phenylalanine*

proline**serinethreonine*tryptophan*tyrosine*valine*

* essential amino acids in animal diets** an imino acid derived from pyrollidine

Amino acid: the amino acids in proteins arealpha amino acids. The COOH group andNH2 group are on the same carbon atom

H

COOHR C

NH2

AMINO ACIDS MOST COMMONLY FOUND IN PROTEINS

aminotoluine See toluidine.

ammonia (NH3) A colorless gas with acharacteristic pungent odor. On cooling andcompression it forms a colorless liquid,which becomes a white solid on furthercooling. Ammonia is very soluble in water(a saturated solution at 0C contains 36.9%of ammonia); the aqueous solution is alka-line and contains a proportion of free am-monia. Ammonia is also soluble in ethanol.It reacts with acids to form ammoniumsalts; for example, it reacts with hydrogenchloride to form ammonium chloride:

NH3(g) + HCl(g) NH4Cl(g)See also amine salt.

ammoniacal Describing a solution inaqueous ammonia.

amount of substance Symbol: n Ameasure of the number of entities presentin a substance. See mole.

AMP (adenosine monophosphate) Anucleotide consisting of adenine, ribose,and phosphate. See ATP.

amphiprotic Able to act as both an ACIDand a base. For example, the amino acidsare amphiprotic because they contain bothacidic (COOH) and basic (NH2) groups.See also amphoteric; solvent.

ampholyte ion See zwitterion.

amphoteric A material that can displayboth acidic and basic properties. The termis most commonly applied to the oxidesand hydroxides of metals that can formboth cations and complex anions. For ex-ample, zinc oxide dissolves in acids to formzinc salts and also dissolves in alkalis toform zincates, [Zn(OH)4]2. Compoundssuch as the amino acids can also be de-scribed as amphoteric, although it is moreusual to use the term AMPHIPROTIC.

amu See atomic mass unit.

amyl group See pentyl group.

amyl nitrite (C5H11ONO) A pale brown

volatile liquid organic compound; a ni-trous acid ester of 3-methylbutanol (iso-amyl alcohol). It is used in medicine as aninhalant to dilate the blood vessels (andthereby prevent pain) in patients withangina pectoris.

amylopectin The water-insoluble frac-tion of STARCH.

amylose A polymer of GLUCOSE; a poly-saccharide sugar that is found in STARCH.

anabolic steroid Any STEROID hormoneor synthetic steroid that promotes growthand formation of new tissue. Anabolicsteroids are used in the treatment of wast-ing diseases. They are also sometimes usedin agriculture to boost livestock produc-tion. People also use them to build up mus-cles, although this is now generally out-lawed in sporting activities.

anabolism All the metabolic reactionsthat synthesize complex molecules frommore simple molecules. See also metabo-lism.

anaerobic Describing a biochemicalprocess that takes place in the absence offree oxygen. Compare aerobic.

anaerobic respiration Respiration inwhich oxygen is not involved. It is found inyeasts, bacteria, and occasionally in muscletissue. In this type of respiration the or-ganic substrate is not completely oxidizedand the energy yield is low. In the absenceof oxygen in animal muscle tissue, glucoseis degraded to pyruvate by GLYCOLYSIS,with the production of a small amount ofenergy and also lactic acid, which may beoxidized later when oxygen becomes avail-able (see oxygen debt). FERMENTATION is anexample of anaerobic respiration, in whichcertain yeasts produce ethanol and carbondioxide as end products. Only two mol-ecules of ATP are produced by this process.Compare aerobic respiration.

analysis The process of determining theconstituents or components of a sample.There are two broad major classes of

17

analysis

analysis, qualitative analysis essentiallyanswering the question what is it? andquantitative analysis answering the ques-tion how much of such and such a compo-nent is present? There is a large number ofanalytical methods that can be applied, de-pending on the nature of the sample andthe purpose of the analysis. These includegravimetric, volumetric, and systematicqualitative analysis (classical wet meth-ods); and instrumental methods, such aschromatographic, spectroscopic, nuclear,fluorescence, and polarographic tech-niques.

ngstrom Symbol A unit of length de-fined as 1010 meter. The ngstrom wasused for expressing wavelengths of light orultraviolet radiation or for the sizes of mol-ecules; the nanometer is now preferred.

anhydride A compound formed by re-moving water from an acid or, less com-monly, a base. Many nonmetal oxides areanhydrides of acids: for example CO2 is theanhydride of H2CO3 and SO3 is the anhy-

dride of H2SO4. Organic anhydrides areformed by removing H2O from two car-boxylic acid groups, giving compoundswith the functional group CO.O.CO.These form a class of organic compoundscalled ACID ANHYDRIDES.

anhydrous Describing a substance thatlacks moisture, or a salt with no water ofcrystallization.

aniline (aminobenzene; phenylamine;C6H5NH2) A colorless oily substancemade by reducing nitrobenzene (C6H5-NO2). Aniline is used for making dyes,pharmaceuticals, and other organic com-pounds.

animal starch See glycogen.

anion A negatively charged ion, formedby addition of electrons to atoms or mol-ecules. In electrolysis anions are attractedto the positive electrode (the anode). Com-pare cation.

ngstrom

18

OC

H3C

HO

OC

HO

H3C

OC

H3C

O

OC

H3C

Anhydride

C

CH2C OH

O

OH

O

H2CC

CH2C

O

O

O

H2C

maleic acid maleic anhydride

Anhydride: a cyclic anhydride

anionic detergent See detergent.

anionic resin An ION-EXCHANGE ma-terial that can exchange anions, such as Cl

and OH, for anions in the surroundingmedium. Such resins are used for a widerange of analytical and purification pur-poses.

They are often produced by addition ofa quaternary ammonium group (N(CH3)4+)or a phenolic group (OH) to a stablepolyphenylethene resin. A typical exchangereaction is:

resinN(CH3)4+Cl + KOH resinN(CH3)4+OH + KCl

Anionic resins can be used to separate mix-tures of halide ions. Such mixtures can beattached to the resin and recovered sepa-rately by elution.

annulene A ring compound containingalternating double and single CC bonds.The compound C8H8, having an eight-membered ring of carbon atoms, is the next

annulene larger than benzene. It is not anAROMATIC COMPOUND because it is not pla-nar and does not obey the Hckel rule.C8H8 is called cyclo-octatetraene. Higherannulenes are designated by the number ofcarbon atoms in the ring. [10]-annuleneobeys the Hckel rule but is not aromaticbecause it is not planar as a result of inter-actions of the hydrogen atoms inside thering. There is evidence that [18]-annulene,which is a stable red solid, has aromaticproperties.

anode In electrolysis, the electrode thatis at a positive potential with respect to thecathode. In any electrical system, such as adischarge tube or electronic device, theanode is the terminal at which electronsflow out of the system.

anomer Either of two isomeric forms ofa cyclic sugar that differ in the dispositionof the OH group on the carbon next tothe O atom of the ring (the anomeric

19

anomer

[14]-annulene

[18]-annulene

H

[30]-annulene

H

H H

H H

H H

H H

H H

H H

H H

H

H H

H

H

H

HH H

H

H

H

H H

H H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

HH

HH

HH

H

H

H HH

H H

Annulene

carbon). Anomers are diastereoisomers.They are designated or according to whether the OH is below or above the ring respectively. See illustration atsugar.

anomeric carbon See anomer.

anthocyanin One of a group of water-soluble pigments found dissolved in higherplant cell vacuoles. Anthocyanins are red,purple, and blue and are widely distrib-uted, particularly in flowers and fruits,where they are important in attracting in-sects, birds, etc. They also occur in buds and sometimes contribute to the au-tumn colors of leaves. They are natural pH indicators, often changing from red to blue as pH increases, i.e. acidity de-creases. Color may also be modified bytraces of iron and other metal salts and or-ganic substances, for example cyanin is redin roses but blue in the cornflower. Seeflavonoid.

anthracene (C14H10) A white crystallinesolid used extensively in the manufactureof dyes. Anthracene is found in the heavy-and green-oil fractions of crude oil and isobtained by fractional crystallization. Itsstructure is benzene-like, having three six-membered rings fused together. The reac-tions are characteristic of AROMATICCOMPOUNDS.

anthracite The highest grade of coal,with a carbon content of between 92% and98%. It burns with a hot blue flame, givesoff little smoke and leaves hardly any ash.

anthraquinone (C6H4(CO)2C6H4) Acolorless crystalline quinone used in pro-ducing dyestuffs such as alizarin.

antibonding orbital See orbital.

anticlinal conformation See confor-mation.

antiknock agent A substance added togasoline to inhibit preignition or knock-ing. A common example is lead tetraethyl,although use of this is discouraged in manycountries for environmental reasons.

antioxidant A substance that inhibitsoxidation. Antioxidants are added to suchproducts as foods, paints, plastics, andrubber to delay their oxidation by atmos-pheric oxygen. Some work by formingchelates with metal ions, thus neutralizingthe catalytic effect of the ions in the oxida-tion process. Other types remove interme-diate oxygen free radicals. Naturallyoccurring antioxidants can limit tissue orcell damage in the body. These includevitamin E and -carotene.

antiperiplanar conformation See con-formation.

apoenzyme The protein part of a conju-gate enzyme. It is an enzyme whose cofac-tor has been removed (e.g. via dialysis)rendering it catalytically inactive. Whencombined with its PROSTHETIC GROUP orcoenzyme it forms a complete enzyme(HOLOENZYME).

aprotic See solvent.

aqueous Describing a solution in water.

arene An organic compound containinga benzene ring; i.e. an aromatic hydrocar-bon or a derivative of an aromatic hydro-carbon.

anomeric carbon

20

Anthracene

O

O5

6

7

8 1

2

3

4

Anthraquinone

arginine See amino acid.

aromatic compound An organic com-pound with characteristic chemical reac-tions, usually containing BENZENE rings inits structure. Aromatic compounds, such asbenzene, have a planar ring of atoms linkedby alternate single and double bonds. Thecharacteristic of aromatic compounds isthat their chemical properties are not thoseexpected for an unsaturated compound;they tend to undergo nucleophilic substitu-tion of hydrogen (or other groups) on thering, and addition reactions only occurunder special circumstances.

The explanation of this behavior is thatthe electrons in the double bonds are delo-calized over the ring, so that the six bondsare actually all identical and intermediatebetween single bonds and double bonds.The pi electrons are thus spread in a mo-lecular orbital above and below the ring.The evidence for this delocalization in ben-zene is that the bond lengths between car-bon atoms in benzene are all equal andintermediate in size between single anddouble bond lengths. Also, if two hydrogenatoms attached to adjacent carbon atomsare substituted by other groups, the com-pound has only one structure. If the bondswere different two isomers would exist.Benzene has a stabilization energy of 150kJ mol1 over the Kekul structure. It ispossible to characterize aromatic behaviorby detecting a ring current in NMR. Cer-tain heterocyclic molecules, such as PYRI-DINE, also have aromatic properties.

The delocalization of the electrons inthe pi orbitals of benzene accounts for theproperties of benzene and its derivatives,which differ from the properties of alkenesand other aliphatic compounds. The phe-nomenon is called aromaticity. A defini-tion of aromaticity is that it occurs incompounds that obey the Hckel rule: i.e.that there should be a planar ring with atotal of (4n + 2) pi electrons (where n is anyinteger). Using this rule as a criterion cer-tain nonbenzene rings show aromaticity.Such compounds are called nonbenzenoidaromatics. Examples are the cyclopentadi-enyl ion C5H5 and the tropyllium ionC7H7+. Other compounds that have a ring

of atoms with alternate double and singlebonds, but do not obey the rule (e.g. cyclo-octatetraene, which has a nonplanar ringof alternating double and single bonds) arecalled pseudoaromatics.

Compare aliphatic compound. See alsoannulene.

aromaticity See aromatic compound.

Arrhenius equation An equation relat-ing the rate constant of a chemical reactionand the temperature at which the reactiontakes place:

k = Aexp(Ea/RT)where A is a constant, k the rate constant,T the thermodynamic temperature inkelvins, R the gas constant, and Ea the ac-tivation energy of the reaction.

Reactions proceed at different rates atdifferent temperatures, i.e. the magnitudeof the rate constant is temperature depend-ent. The Arrhenius equation is often writ-ten in a logarithmic form, i.e.

logek = logeA E/2.3RTThis equation enables the activation en-

ergy for a reaction to be determined. It isnamed for the Swedish chemist Svante Au-gust Arrhenius (18591927).

Arrhenius theory See acid.

aryl group An organic group derived byremoving a hydrogen atom from an aro-matic hydrocarbon or derivative. Thephenyl group, C6H5, is the simplest exam-ple.

ascorbic acid See vitamin C.

asparagine See amino acid.

aspartic acid See amino acid.

aspirin (acetylsalicylic acid; C9H8O4) Acolorless crystalline compound made bytreating salicylic acid with ethanoyl hy-dride. It is used as an analgesic and anti-pyretic drug, and small doses areprescribed for adult patients at risk of heartattack or stroke. It should not be given tochildren.

21

aspirin

association The combination of mol-ecules of a substance with those of anotherto form more complex species. An exampleis a mixture of water and ethanol (whichare termed associated liquids), the mol-ecules of which combine via hydrogenbonding.

asymmetric atom See chirality; iso-merism; optical activity.

atactic polymer See polymerization.

atmosphere A unit of pressure definedas 101 325 pascals (atmospheric pressure).The atmosphere is used in chemistry onlyfor rough values of pressure; in particular,for stating the pressures used in high-pressure industrial processes.

atom The smallest part of an elementthat can exist as a stable entity. Atoms con-sist of a small dense positively charged nu-cleus, made up of neutrons and protons,with electrons in a cloud around this nu-cleus. The chemical reactions of an elementare determined by the number of electrons(which is equal to the number of protons inthe nucleus). All atoms of a given elementhave the same number of protons (the pro-ton number). A given element may havetwo or more isotopes, which differ in thenumber of neutrons in the nucleus.

The electrons surrounding the nucleusare grouped into shells i.e. main orbitsaround the nucleus. Within these main or-bits there may be subshells. These corre-spond to atomic orbitals. An electron in anatom is specified by four quantum num-bers:1. The principal quantum number (n),

which specifies the main energy levels. ncan have values 1, 2, etc. The corre-sponding shells are denoted by letters K,L, M, etc., the K shell (n = 1) being thenearest to the nucleus. The maximumnumber of electrons in a given shell is2n2.

2. The orbital quantum number (l), whichspecifies the angular momentum. For agiven value of n, l can have possible val-ues of n1, n2, 2, 1, 0. For instance,the M shell (n = 3) has three subshells

with different values of l (0, 1, and 2).Sub-shells with angular momentum 0, 1,2, and 3 are designated by letters s, p, d,and f.

3. The magnetic quantum number (m).This can have values l, (l 1) 0 + (l l), + l. It determines the orientationof the electron orbital in a magneticfield.

4. The spin quantum number (ms), whichspecifies the intrinsic angular momen-tum of the electron. It can have values+ and .

Each electron in the atom has four quan-tum numbers and, according to the Pauliexclusion principle, no two electrons canhave the same set of quantum numbers.This explains the electronic structure ofatoms.

atomicity The number of atoms permolecule of an element. Helium, for exam-ple, has an atomicity of one, nitrogen two,and ozone three.

atomic mass unit (amu) Symbol: u Aunit of mass used for atoms and molecules,equal to 1/12 of the mass of an atom of carbon-12. It is equal to 1.660 33 1027kg.

atomic number See proton number.

atomic orbital See orbital.

atomic weight See relative atomic mass(r.a.m.).

ATP (adenosine triphosphate) The uni-versal energy carrier of living cells. Energyfrom respiration or, in photosynthesis,from sunlight is used to make ATP fromADP. It is then reconverted to ADP in var-ious parts of the cell by enzymes known asATPases, the energy released being used todrive three main cellular processes: me-chanical work (muscle contraction and cel-lular movement); the active transport ofmolecules and ions; and the biosynthesis ofother molecules. It can also be converted tolight, electricity, and heat.

ATP is a nucleotide consisting of ade-nine and ribose with three phosphate

association

22

groups attached. Hydrolysis of the termi-nal phosphate bond releases energy(30.6 kJ mol1) and is coupled to anenergy-requiring process. Further hydroly-sis of ADP to AMP sometimes occurs, re-leasing more energy. The pool of ATP issmall, but the faster it is used, the faster itis replenished. ATP is not transportedaround the body, but is synthesized whereit is needed.

atto- Symbol: a A prefix denoting 1018.For example, 1 attometer (am) = 1018

meter (m).

autocatalysis See catalyst.

autoclave An apparatus consisting of anairtight container whose contents areheated by high-pressure steam; the con-tents may also be agitated. Autoclaves areused for reactions between gases underpressure in industrial processing and forsterilizing objects.

auxin Any of a group of plant hor-mones, the most common naturally occur-ring one being indole acetic acid, IAA.Auxins are made continually in growingshoot and root tips. Synthetic auxins,cheaper and more stable than IAA, are em-ployed in agriculture, horticulture, andresearch. These include indoles and naph-thyls: e.g. NAA (naphthalene acetic acid)used mainly as a rooting and fruit settinghormone; phenoxyacetic acids, e.g. 2,4-D(2,4-dichlorophenoxyacetic acid) used asweed-killers and modifiers of fruit develop-ment; and more toxic and persistent ben-zoic auxins, e.g. 2,4,5-trichlorobenzoic

acid, also formerly used as herbicides butnow widely restricted.

Avogadro constant (Avogrado number)Symbol: NA The number of particles in onemole of a substance. Its value is 6.022 52 1023 mol1.

Avogadro number See Avogadro con-stant.

Avogadros law The principle thatequal volumes of all gases at the same tem-perature and pressure contain equal num-bers of molecules. It is often calledAvogadros hypothesis. It is strictly trueonly for ideal gases.

axial conformation See cyclohexane.

azeotrope (azeotropic mixture) A mix-ture of liquids for which the vapor phasehas the same composition as the liquidphase. It therefore boils without change incomposition and, consequently, withoutprogressive change in boiling point.

The composition and boiling points ofazeotropes vary with pressure, indicatingthat they are not chemical compounds.Azeotropes may be broken by distillationin the presence of a third liquid, by chemi-cal reactions, adsorption, or fractionalcrystallization. See constant-boiling mix-ture.

azeotropic distillation A method usedto separate mixtures of liquids that cannotbe separated by simple distillation. Such amixture is called an azeotrope. A solvent isadded to form a new azeotrope with one ofthe components, and this is then removedand subsequently separated in a secondcolumn. An example of the use of azeo-tropic distillation is the dehydration of96% ethanol to absolute ethanol.Azeotropic distillation is not widely usedbecause of the difficulty of finding inex-pensive nontoxic noncorrosive solventsthat can easily be removed from the newazeotrope.

azeotropic mixture See azeotrope.

23

azeotropic mixture

- --

N

N N

N

OCH2O

OOO

OOO

P O P O P O

NH2

OHOH

-

ATP

azide 1. An organic compound of gen-eral formula RN3.2. An inorganic compound containing theion N3.

azine An organic heterocyclic com-pound that has a hexagonal ring contain-ing carbon and nitrogen atoms. Pyridine(C5H5N) is the simplest example.

azo compound A type of organic com-pound of the general formula RN:NR,where R and R are aromatic groups. Azocompounds can be formed by coupling aDIAZONIUM COMPOUND with an aromaticphenol or amine. Most are colored becauseof the presence of the azo group N:N.

azo dye An important type of dye used

in acid dyes for wool and cotton. The dyesare azo compounds; usually sodium saltsof sulfonic acids.

azo group See azo compound.

azulene (C10H8) A blue crystalline com-pound having a seven-membered ringfused to a five-membered ring. It convertsto naphthalene on heating.

azide

24

1

2

34 5

6

78

Azulene

25

backbiting A process that can occur incertain free-radical POLYMERIZATION reac-tions, in which a radical with an unpairedelectron on the end of the chain convertsinto one in which the unpaired election isnot at the end of the chain. For example,the radical

RCH2CH2CH2CH2CH2 CH2may convert into

RCH2CHCH2CH2 CH2CH3Effectively, this involves a transfer of a

hydrogen atom within the molecule. Typi-cally, the free electron moves from the endof the chain to atom five, counting fromthe end. This is because the process in-volves a transition state with a six-mem-bered ring. The new free radical is morestable than the original one. Further poly-merization occurs at the new unpairedelectron leading to the production of poly-mers with butyl (CH3CH2CH2CH2) sidechains.

Baeyer, Johann Friedrich WilhelmAdolph von (18351917) German or-ganic chemist. Baeyer worked mainly in or-ganic synthesis and is noted for his study ofthe dye indigo. He started his work on in-digo in 1865 and continued for 20 years;he determined the structure of indigo in1883. The structure he postulated was cor-

rect (except for the stereochemistry of thedouble bond, which was subsequentlyshown by x-ray crystallography to betrans). Baeyer discovered a number of sub-stances including barbituric acid. His laterinvestigations on ring compounds andpolyacetylenes led him to consider the sta-bility of carboncarbon bonds in cycliccompounds. This resulted in the Baeyerstrain theory. Baeyer was awarded the1905 Nobel Prize for chemistry for hiswork on indigo and aromatic compounds.

BaeyerVilliger reaction A type of re-action in which a ketone reacts with a per-oxy acid, with resulting production of anester. For example,

RCOR RCOOR.The reaction involves insertion of an oxy-gen atom next to the carbonyl (CO) group.Typical peroxy acids used are trifluoro-perethanoic acid (CF3.CO.O.OH) andmeta-chloroperbenzoic acid (m-CPBA;ClC6H4.CO.O.OH). The reaction was dis-covered in 1899 by the German chemistsA. Baeyer and V. Villiger, and is commonlyused in organic synthesis. In certain caseshydrogen peroxide (H2O2) can be used asthe oxidizing agent. This is sometimesknown as the Dakin reaction. The BaeyerVilliger reaction is a type of rearrange-

B

C

CH2

CH2C

C

H

H2

H2

H

CH2R

CH3

C

CH2

CH2

C

H2H

CH2R

Backbiting

ment. For a peroxy acid X.CO.O.OH,there is an intermediate cation formedR2C+(OH)(O.CO.X). The mechanism in-volves migration of a group R onto theoxygen of the peroxy acid group.

Bakelite (Trademark) A common ther-mosetting synthetic polymer formed by thecondensation of phenol (C6H5OH) andmethanal (formaldehyde, HCOH). It is anexample of a phenolic resin (or phenolformaldehyde resin), and was one of thefirst useful synthetic polymers. The reac-tion between phenol and methanal occursunder acid conditions and involves elec-trophilic substitution on the benzene ringto give a three-dimensional polymericstructure. Bakelite is named for the Bel-gian-born US chemist Leo Hendrik Baeke-land (18631944), who discovered it in1909.

ball mill A device commonly used in thechemical industry for grinding solid ma-terial. Ball mills usually have slowly rotat-ing steel-lined drums containing steel balls.The material is crushed by the tumbling ac-

tion of the balls in the drum. Comparehammer mill.

banana bond (bent bond) In strained-ring compounds the bond angles thatwould be produced by hybridization of or-bitals are not equal to the angles obtainedby joining the atomic centers. In such casesit is sometimes assumed that the bondingorbital is bent or banana-like in shape. Forexample, in cyclopropane the three carbonatoms are arranged in an equilateral trian-gle, and the bond angle is 60. The sp3 hy-bridization gives an angle of about 104between the orbitals. Consequently, the or-bitals overlap at an angle, giving a bananabond. The term banana bond is also usedin a quite separate sense for a multicenterbond of the type present in electron-deficient compounds such as diborane(B2H6).

band spectrum A SPECTRUM that ap-pears as a number of bands of emitted orabsorbed radiation. Band spectra are char-acteristic of molecules. Often each bandcan be resolved into a number of closelyspaced lines. The different bands corre-

Bakelite

26

CH2

CH2 CH2

CH2

OH OH

OH OH

OH

OH

CH2 CH2

CH2

Bakelite

spond to changes of electron orbit in themolecules and the closely spaced lines ineach band, seen under higher resolution,are the result of different vibrational statesof the molecule.

barrel A measurement of volume oftenused in the oil and chemical industries. Onebarrel is equal to 159 liters (about 29 USgallons).

Barton, Sir Derek Harold Richard(191898) British organic chemist notedfor his work on the stereochemistry of or-ganic molecules, particularly natural prod-ucts. In a major paper published in 1950 hesuggested that the rates of reactions in iso-mers are strongly influenced by the spatialorientations of their functional groups.This paper initiated the branch of organicchemistry known as conformational analy-sis. Barton studied many natural products,including phenols. In 1959 he developed asimple synthesis for the hormone aldos-terone. He shared the 1969 Nobel Prize forchemistry with Norwegian chemist OddHassell.

base See acid.

base analog An unnatural purine orpyrimidine that can be incorporated intoDNA, causing altered base pairing. Somebase analogs are used therapeutically asanticancer drugs.

base-catalyzed reaction A reactioncatalyzed by bases. Typical base-catalyzedreactions are the CLAISEN CONDENSATIONand the ALDOL REACTION, in which the firststep is abstraction of a proton to give acarbanion.

base pairing The linking together of thetwo helical strands of DNA by bonds be-tween complementary bases, adenine pair-ing with thymine and guanine pairing withcytosine. The specific nature of base pair-ing enables accurate replication of thechromosomes and thus maintains the con-stant composition of the genetic material.In pairing between DNA and RNA theuracil of RNA pairs with adenine.

basic Acting as a base; having a ten-dency to release hydroxide ions (OH) inaqueous solution. A basic solution has anexcess of OH ions over H+ ions; i.e. a pHgreater than 7.

batch process A manufacturing processin which the reactants are fed into theprocess in fixed quantities (batches), ratherthan in a continuous flow. At any particu-lar instant all the material, from its prepa-ration to the final product, has reached adefinite stage in the process. Such processespresent problems of automation and in-strumentation and tend to be wasteful ofenergy. For this reason, batch processing isused on an industrial scale only when smallquantities of valuable or strategic materialsare required, e.g. specialist chemicals orpharmaceuticals. Compare continuousprocess.

Beckmann rearrangement A type ofreaction in which the OXIME of a ketone isconverted into an amide using a sulfuricacid catalyst. First discovered by the Ger-man chemist Ernst Beckmann (18531923), it is used in the manufacture ofpolyamides (see nylon).

Beckmann thermometer A type ofmercury thermometer designed to measuresmall differences in temperature ratherthan scale degrees. Beckmann thermome-ters have a larger bulb than common ther-mometers and a stem with a small internaldiameter, so that a range of 5C coversabout 30 centimeters in the stem. The mer-cury bulb is connected to the stem in sucha way that the bulk of the mercury can beseparated from the stem once a particular5 range has been attained. The thermome-ter can thus be set for any particular range.The Beckmann thermometer has com-monly been used for measuring such quan-tities as depression of freezing point andelevation of boiling point.

bent bond See banana bond.

benzaldehyde See benzenecarbalde-hyde.

27

benzaldehyde

benzene (C6H6) A colorless liquid hy-drocarbon with a characteristic odor. Ben-zene is a highly toxic compound andcontinued inhalation of the vapor is harm-ful. It was originally isolated from coal tarand for many years this was the principalsource of the compound. Contemporarymanufacture is from hexane; petroleumvapor is passed over platinum at 500Cand at a pressure of 10 atmospheres:

C6H14 C6H6 + 4H2Benzene is the simplest aromatic hydro-

carbon. See aromatic compound. Thestructure of benzene was the subject ofconsiderable speculation in the 19th cen-tury. The basic problem known as thebenzene problem was that of reconcilingthe formula of benzene, C6H6, with itschemical reactions. The empirical formulais the same as that of acetylene, C2H2, and

benzene

28

(a) (b) (c) (d)

(e) (f) (g)

Benzene: early structures suggested for benzene: (a) Kekul (1865); (b) Claus (1867); (c) Dewar(1867); (d) Ladenburg (1869); (e) Kekul (1865); (f) ArmstrongBaeyr (1887); (g) Thiele (1899)

HH

H H

CC

CC

Benzene: in benzene, 6 p orbitals can combine in different ways to give delocalized molecularorbitals. The one of lowest energy has two donut-shaped areas above and below the ring ofcarbon atoms.

it might be expected that benzene wouldundergo similar reactions. However, ben-zene does not show the usual behavior of acompound containing double or triplebonds.

For example, acetylene adds bromine toyield CHBr:CHBr and eventually CHBr2-CHBr2. Benzene, with an iron bromide cat-alyst, suffers displacement of one of itshydrogen atoms to yield C6H5Br. This typeof activity in which substitution reactionsoccur indicates that benzene might be satu-rated.

Benzene, however, does not always actas a saturated compound. In sunlightbromine is added to give C6H6Cl6 and hy-drogen can also be added with a nickel cat-alyst to yield cyclohexane, C6H12. Anumber of different formulae were put for-ward to try to explain the properties. In1865 the German chemist August Kekul(182996) suggested a structure with alter-nate double and single bonds in a hexago-nal ring. To account for the fact thatbenzene has only three disubstitution prod-ucts, he further proposed that the positionsof the bonds oscillate so that two moleculesare in equilibrium. This structure theKekul formula is the one often used informulae of compounds containing ben-zene rings.

The modern idea of aromaticity isbased not on equilibrium between Kekulstructures but on RESONANCE betweenthem. The bonds in benzene have charac-ters between double and single bonds: thecarbon atoms are held together by six sin-gle bonds and the remaining six electrons,from the double bonds, are delocalized

over the ring. This is the reason benzenehas all its C-C bonds of the same lengthand undergoes ELECTROPHILIC SUBSTITUTIONreactions.

benzenecarbaldehyde (benzaldehyde;C6H5CHO) A yellow oily ALDEHYDEwith a distinct almondlike odor (the com-pound occurs in almond kernels). Ben-zenecarbaldehyde may be synthesized inthe laboratory by the usual methods ofaldehyde synthesis. It is used as a food fla-voring and in the manufacture of dyes andantibiotics, and can be readily manufac-tured by the chlorination of methylbenzene(toluene) on the methyl group and thesubsequent hydrolysis of dichloromethyl-benzene:

C6H5CH3 + Cl2 C6H5CHCl2C6H5CHCl2 + 2H2O C6H5CH(OH)2

+ 2HClC6H5CH(OH)2 C6H5CHO + H2O

benzenecarbonyl chloride (benzoylchloride; C6H5COCl) A liquid acyl chlo-ride used as a benzoylating agent. See acy-lation.

29

benzenecarbonyl chloride

Cl

Cl

Cl

Cl

Cl

Cl

1,1-dichlorobenzene(o-dichlorobenzene)

1,2-dichlorobenzene(m-dichlorobenzene)

1,3-dichlorobenzene(p-dichlorobenzene)

Benzene: disubstituted derivates of benzene

HC

CH

HC

HC CH

CH

O

Benzenecarbaldehyde (benzaldehyde)

benzenecarbonyl group

30

benzenecarbonyl group (benzoylgroup) The group C6H5CO.

benzenecarboxylic acid (benzoic acid;C6H5COOH) A white crystalline car-boxylic acid found naturally in someplants. It is used as a food preservative. Thecarboxyl group (COOH) directs furthersubstitution onto the benzene ring in the 3position.

benzene-1,2-dicarboxylic acid (ph-thalic acid; C6H4(COOH)2) A whitecrystalline aromatic acid. On heating itloses water to form phthalic anhydride,which is used to make dyestuffs and poly-mers.

benzene-1,4-dicarboxylic acid (tereph-thalic acid; C6H4(COOH)2) A colorlesscrystalline organic acid used to produceDacron and other polyesters.

benzene-1,3-diol (resorcinol; C6H4(OH)2)A white crystalline phenol used in the man-ufacture of dyestuffs and celluloid.

benzene-1,4-diol (hydroquinone; quinol;C6H4(OH)2) A white crystalline phenolused in making dyestuffs. See also quinone.

benzene ring The cyclic hexagonalarrangement of six carbon atoms that arecharacteristic of benzene and its deriva-tives. See aromatic compound; benzene.

benzenesulfonic acid (C6H5SO2OH) Awhite crystalline sulfonic acid made by sul-fonation of benzene. Any further substitu-tion onto the benzene ring is directed intothe 3 position.

benzfuran (coumarone; C8H6O) A crys-talline compound having a benzene ringfused to a furan ring.

benzilic acid rearrangement A reac-tion in which benzil (1,2-diphenylethan-1,2-dione) is treated with hydroxide andthen with acid to give benzilic acid (2-hy-droxy-2,2-diphenylethanoic acid):

C6H5.CO.CO.C6H5 (C6H5)2C(OH).COOH

The reaction, which involves migration ofa phenyl group (C6H5) from one carbonatom to another, was the first rearrange-ment reaction to be described (by Germanchemist Justus von Liebig in 1828).

benzoic acid See benzenecarboxylicacid.

benzole A mixture of mainly aromatichydrocarbons obtained from coal.

benzopyrene See benzpyrene.

benzoquinone See quinone.

benzoylation The introduction of abenzoyl group (benzenecarbonyl group)into a compound. See acylation.

benzoyl chloride See benzenecarbonylchloride.

benzoyl group See benzenecarbonylgroup.

benzpyrene (benzopyrene; C20H12) Acyclic aromatic hydrocarbon with a struc-ture consisting of five fused benzene rings.It occurs in coal tar and is produced by in-complete combustion of some organiccompounds. Benzpyrene, which is presentin tobacco smoke, has marked carcino-genic properties.

3

2

1

OOO6

5

4

Benzfuran (coumarone)HC

CH

HC

HC CH

C

O

OH

Benzenecarboxylic acid (benzoic acid)

benzpyrrole See indole.

benzyl alcohol See phenylmethanol.

benzyl group The group C6H5CH2.

benzyne (C6H4) A short-lived interme-diate present in some reactions. The ring ofsix carbon atoms contains two doublebonds and one triple bond (the systematicname is 1,2-didehydrobenzene).

Bergius process A process formerlyused for making hydrocarbon fuels fromcoal. A mixture of powdered coal, heavyoil, and a catalyst was heated with hydro-gen at high pressure.

beta-pleated sheet A type of PROTEINstructure in which polypeptide chains runclose to each other and are held together byhydrogen bonds at right angles to the mainchain. The structure is folded in regularpleats. Fibres having this type of structureare usually composed of amino acids withshort side chains. The chains may run inthe same direction (parallel) or opposite di-rections (antiparallel). It is one of the twobasic secondary structures of proteins.

bi- Prefix meaning two. For example,biphenyls are compounds that have twophenyl groups joined together, as inC6H5C6H5. The prefix is also commonlyused in naming inorganic compounds toindicate the presence of hydrogen; for in-stance, sodium bisulfate (NaHSO4) issodium hydrogensulfate, etc.

bicarbonate See hydrogencarbonate.

bimolecular Describing a reaction or astep in a reaction that involves two mol-ecules, ions, etc. For example the decom-position of hydrogen iodide,

2HI H2 + I2takes place between two molecules and istherefore a bimolecular reaction. All bi-molecular reactions are second order, butsome second-order reactions are not bi-molecular. See also order.

binary compound A chemical com-

31

binary compound

Benzyne

Benzpyrene

A

A

A

AA

A

A

A

A

A

A

A

A

A

A

A

Beta-pleated sheet

pound formed from only two elements.Water (H2O) and sodium chloride (NaCl)are examples.

bioassay An experimental technique formeasuring quantitatively the strength of abiologically active chemical by its effect ona liv